MINIMIZER SLOWLY MOVING ATOMS WITH BAD CONTACTS DOWNHILL

From: David Tanner (dtanner_at_ks.uiuc.edu)
Date: Wed Mar 25 2009 - 12:47:44 CDT

While trying to minimize a solvated structure of 70,000 atoms, the
minimizer seems to be stuck on

MINIMIZER SLOWLY MOVING ATOMS WITH BAD CONTACTS DOWNHILL
PRESSURE: 3317 1.27788e+08 766912 1.61734e+06 766912 1.26235e+08
1.56142e+06 1.61734e+06 1.56142e+06 1.26205e+08
GPRESSURE: 3317 1.31167e+08 1.59921e+06 1.8525e+06 15885 1.28542e+08
1.52692e+06 1.4571e+06 929851 1.29431e+08
ENERGY: 3317 186524.4117 20803.2311 762.8600
131.4044 -89412.6070 69834715.6227 0.0000 0.0000
       0.0000 69953524.9229 0.0000 69953524.9229
69953524.9229 0.0000 126742829.0978 129712883.2452
153900.0000 126742829.0978 129712883.2452

Within 10 steps, the energy was minimized to what you see here, but
after another 3000 steps nothing has not improved (and it won't write
to DCD for me to view what's happening). Similar systems of mine
minimized just fine: "MSMAWBCD" stopped being displayed well before
3000 steps, and other minimizations ensued.

Should "MSMAWBCD" take this long or does this suggest there is
something wrong with my structure.

What would the most likely structural problems be? Could I have the
wrong atoms bonded; my structure looked correct when I checked it?
Could atoms be overlapping in such a way that they cannot pulled
apart?

Thank you,
David E. Tanner

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
David E. Tanner
Theoretical and Computational Biophysics Group
3159 Beckman Institute
University of Illinois at Urbana-Champaign
405 N. Mathews
Urbana, IL 61801
(217) 244 - 2905
dtanner_at_ks.uiuc.edu
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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